Let's say site_name is settable both per-domain and per-language.
On page /admin/config/system/variable/edit/variable_realm_list_[variable_realm] I see site_name listed in the "Domain" and "Language" relams, but "Domain+Language" is empty and has no Edit link in the list at /admin/config/system/variable/realm.
Worse, trying to edit the variable (at /admin/config/system/variable/edit/site_name) does tell me that this variable is supposed to be both domain- and language-specific, but this form in fact changes the global default value for that variable – no matter which entry in the "Check you are editing the variables for the right Language value or select the desired Language." (or Domain) lists is active.
This is misleading and thus broken. As it is, this dialog is mostly useless.
The most reasonable fix for this would probably be to drop the realm-specific edit screens. They're mostly-useless and confusing. Instead, add a "default" entry to the select-the-desired-whatever frames on the /admin/config/system/variable/edit/* page, and get that page to actually work as shown. For bonus points, show a list of realms and the value of that variable in these realms, and display a "delete and revert to default" button if any non-default realm component is selected.
Feel free to split off a feature request for that; as this is a bug report, the minimal fix would be the "get that page to actually work as shown" part in the preceding paragraph. until that time I'll use phpmyadmin if I want to change one of these variables. :-/